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223 Cards in this Set
- Front
- Back
- 3rd side (hint)
# of gametes from a triploid producing that will be haploid?
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(1/2)^n, n= # chromosomes
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Monosomy
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2N-1
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Nullisomy
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2N-2
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Trisomy
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2N+1
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Tetrasomy
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2N+2
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euploid
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an organism or cell has one complete set of chromosomes or an exact multiple of complete sets
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aneuploid
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an organism or cell has a chromosome number that is not an exact multiple of the haploid set of chromosomes.
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autopolyploidy
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all the sets of chromosomes originate in the same species
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Example of autopolyploidy (think of a fruit we talked about in class)
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3n banana- diploid fused with haploid.
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allopolyploidy
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the sets of chromosomes involved come from different, though usually related, species
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Example of allopolyploidy animal (think horses and donkeys)
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Mule- sterile
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How can allopolyploid hybrids be fertile?
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Rarely, through a division error, the two sets of chromosomes double, producing 2N1 + 2N2. Each diploid set can function normally in meiosis, so such fusion of two gametes can produce fully fertile, allotetraploid, 2N1 + 2N2 hybrids.
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epigenetics
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a heritable change in gene expression that occurs without a change in DNA sequence
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Barr body
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a highly condensed mass of chromatin
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genetic mosaic
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Some cells show the phenotypes of one X chromosome, and the other cells show the phenotypes of the other X chromosome. (Mammalian females that are heterozygous for X-linked traits are genetic mosaics due to X inactivation.)
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Example of genetic mosaic
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calico cats- orange parent and black parent
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# Barr bodies = ?
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# X chromosomes - 1
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dosage compensation
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in female mammals, inactivating one of the two X chr0s in somatic cells at an early state in development, leaving only 1 X chr0 transcriptionally active.
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convergent evolution
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similar phenotypes can evolve in organisms that are distantly related
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rooted tree
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where it is possible to distinguish one internal node as representing a common ancestor to all the other nodes on a tree
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Gene conversion
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the DNA sequence of an allele on one homolog is copied and replaces the DNA sequence of the allele on the other homolog (a process of genetic recombination in meiosis) (non-reciprocal)
Eg. A allele on one homology replicates and replaces the a alele on the other homolog, resulting in both homologs now having A alleles. |
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Parsimony-Based Approach
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assume that the simplest tree (one with the fewest # of mutations) is considered to be the best and is deemed a tree of maximum parsimony.
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Anaphase I
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homolog separation is initiated by loss of sister chromatid adhesion
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Coefficient of Coincidence
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(#Obs d-COs)/(# Exp d-COs)
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Interference Complete
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Interference = 1, within 10 mu. No COs within 10 mu
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Anaphase I
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homolog separation is initiated by loss of sister chromatid adhesion
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Coefficient of Coincidence
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(#Obs d-COs)/(# Exp d-COs)
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Interference Complete
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Interference = 1, within 10 mu. No DOUBLE COs within 10 mu
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Accurate genetic map
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No 2 adjacent markers should be greater than 10 mu apart
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NPD << PD
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Genes are cis-linked
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NPD = PD
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Genes are on different chr0s (trans/repulsion)
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# COs to get PD?
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0
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# COs to get NPD?
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a double crossover results in a fraction of NPD (unless it only involves two of the chromatids)
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Recombination Frequency
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(NPD/Total) x 100%
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Gene conversion & crossing over
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About 50% of the time conversion is associated with a CO
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1st gene mapped using modern DNA technology
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Huntington's Disease gene
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Human genome
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3,000 x 10^6 base pairs
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Polymorphism
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presence of more than 1 common form in a population (eg. height)
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Restriction enzymes
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recognize specific DNA sequences (usually palindromic)
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Southern Blotting
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1. Digest DNA w/ restriction enzyme
2. Sep fragments with Gel Electrophoresis 3. Denature DNA by soaking gel in base sol'n 4. Blot DNA onto nitrocellulose (binds ss-DNA but not ds-DNA). Single-strand DNA migrates up nitrocellulose. 5. Block filter by incubating nitrocellulose with a vast excess of ss-DNA 6. Hybridize filter to a ss-radioactive "probe" DNA derived from a human DNA clone. Probe will stick to complementary ss-DNA. 7. Wash blot, expose it to film & develop film |
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autoradiogram
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film after being exposed to Southern blot with radioactive probe on it
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Founder effect
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alteration in allele frequency due to the founding of a population by a small # of individuals.
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Huntingtin Protein
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run of glutamines encoded by CAG.
Normal run: 10-35 HD protein: 42-121 |
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Polyglutamine
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run of glutamines
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Drosophila's salivary gland chromosomes?
# chromosomes in each cell? |
Permanently in Interphase. Undergo 10 rounds of replication with no cell division.
2^10 = 1024 chromatids/chr0s in each cell |
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del(5)p15/+ (heterozygote)
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show cri du chat
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Heterozygotes for deficiencies are typically Normal/Abnormal?
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Abnormal
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Complementation
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production of normal phenotype when 2 mutations are combined in trans in diploid
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Crossing-over at telomeres and centromeres increase/decrease
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Decrease. Suppressed.
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multigene families
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sets of related genes that have evolved from some ancestral gene through gene duplication
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unequal C-O
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misalignment of sequences during CO between homologs, causes gene duplications and deletions
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Colorblindness caused by?
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unequal CO
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Paracentric Inversion
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both breakpoints lie on same side of centromere
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Pericentric Inversion
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the breakpoints lie on opposite sides of centromere
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Drosophila males CO or no?
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No COs
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Paracentric inversions appear to express/suppress CO?
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Suppress. Non-CO chromatids are directed to the functional egg nucleus
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Pericentric inversions appear to express/suppress CO?
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Suppress because inviable progeny die and aren't seen
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Heterozygosity for Pericentric Inversions reduce fertility or no?
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Reduce fertility
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CO occurs in which phase?
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Pachytene
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Adjacent I segregation
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TI + N2 <--> T2 + N1
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Adjacent II segregation
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TI + NI <--> T2 + N2
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Adj I + Adj II = ?
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1/2 of segregation
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Alternate Segregation
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TI + T2 <--> N1 + N2
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Adjacent Segregation chiasma shape
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planar ring
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Alternate Segregation chiasma shape
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figure-8
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Adj & Alt Segregation Progeny Results? (Viable and inviable ratio)
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account for 50% but all progeny die (they did Adj Segregation)
50% but all progeny live (they did Alt Segregation) |
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Translocation hetero x Normal --> Progeny appearance/ratio?
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50% zygote death, see semi-sterility
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pseudolinkage
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Apparent linkage of genes that are on different chr0s. Occurs because the zygotes that didn't inherit the genes together died and aren't seen.
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2n + large duplication = dead/alive?
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Dead. Lethal.
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2n + whole haploid set = Dead/alive?
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Often viable
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colchicine
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binds to tubulin (monomer of microtubles). Prevents the polymerization of tubulin. No spindle = No mitotic division
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How to control euploids?
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Treat euploid with colchicine so that cell goes through replication without division. When ready to see new euploid, wash out colchicine.
Eg 1. 2n cell + colchicine ---> 4n (wash out colchicine) ---> see 4n (2 4N daughters) Eg 2: 2n cell + colchicine ---> 4n...+ colchicine ---> 8n...+ colchicine ---> 16N...wash out colchicine ---> See 16N. |
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Univalents
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unpaired chr0s in Prophase I
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Robertsonian
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Long arm of chr0-14 (or 15) translocated and fused to chr0-21
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Amniocentesis
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stick a needle in uterus to get amniotic fluid of baby (at 16-18 wks)
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Women- oocytes stop at which step? What is happening?
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Oocytes get to diplotene and arrest. At diplotene, chr0s repel from each other but centromeres are holding chr0s together
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What happens to woman's oocytes after age 40?
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Homologs in Diplotene stage fall apart and meiosis is not correct (lose bivalents)
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Heterochromatin
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chromosomes that remain condensed throughout cell cycle
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Facultative heterochromatin
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Heterochromatin condensed in some cells but not others. Represents inactivated segments of euchromatin.
Eg. Barr body (inactivated X chr0 in somatic cells of XX mammalian females) |
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Constitutive heterochromatin
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always condensed in Interphase. Located near centromeres. Present in all cells at identical positions on both homologous chr0s of a pair. (Centromeres and telomeres)
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Goal of Evolutionary Theory
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A scientific explanation for natural history of life
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2 "Threats" of Evolution as a Scientific Theory (Name the guy too)
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(Lewentin 2005)
1. "Fit of hostility"- Creationist challenge - Fundamental belief 2. "Fit of enthusiasm"- expands explanatory scheme to human culture and ideas |
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Darwin's birthday
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2/12/1809
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Darwin was rich/poor? How?
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Rich- inherited his mother's and cousin (his wife)'s fortune
Name of his fortune? |
Wedgewood Pottery fortune
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Darwin's occupation
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Independent Industrialist
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What was the name of society/culture of Darwin?
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Industrialist Revolution
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What role did Darwin play on the Voyage of the Beagle? Purpose of trip?
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a. "Naturalist"
b. To map out shipping routes back to England |
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2 books Darwin brought on the Beagle journey?
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Principles of Geology by Lyell and Milton's Paradise Lost
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Main idea associated with Lyell and Geology?
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Uniformitarianism
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Uniformity of Law
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the assumption that laws of chemistry and physics are unchanged through earth's geological history
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Uniformity of Process
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familiar geological processes to explain past events
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Gradualism
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Idea that geological changes (mountains, sea, grand Canyon) occur in small increments, which accumulate through time to produce large changes.
Another definition: denotes testable hypotheses both in Lyellian geology and Darwinian evolutionary biology |
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Catastrophism (name of guy?) definition
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big, abrupt changes in geology
(Cuvier) |
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Non-directionalism
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dynamic steady state
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What happened at the Cretaceous-Tertiary boundary?
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a point in geological records of mass extinction- extinction of dinosaurs
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How to determine how long ago clay was deposited at Cretaceous-Tertiary (K-T) boundary?
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Measure the amount of iridium in clay. (Iridium comes every year from meteor rock)
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Theory of Impact Crises
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There was an asteroid bombardment onto the Earth that caused a ton of iridium to be on Earth all of a sudden (messed up geological dating by using iridium)
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Domain of Darwinism
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diversity of plant and animal life after it was formed
(NOT origin of life theory) |
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Neo-Darwinism
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Darwinism and chromosomal theory of Inheritance
- rejects Lamarckism = ? |
Larmarkism: that acquired characteristics are inheritable
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Who was Thomas Huxley ?
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Darwin's advocate/ Darwin's Bulldog
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What did Thomas Huxley assert?
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Supernatural is not a part of current science
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developmental module
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characteristic pattern of gene expression and cellular proliferation/differentiation subject to evolution by heterotopy
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SNP
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polymorphism for single base pair change
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population
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focal of Darwinian evolutionary processes
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hybrid DNA
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contains DNA strands from 2 different homologs
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transposition
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insertion of chromosomal segment into new location
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synapomorphy
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diagnostic criteria for a clade
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polytene band
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chromomere
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CVS
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Chorionic villus sampling) sampling of fetal tissue from placenta
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uniformitarianism
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denotes Lyell's principle of geology
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5-methylcytosine
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produced by DNA methyltransferase after DNA replication
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chromatid interference
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lack of responsibility for recombination frequency 50% at maximum. (States that recombination freq can equal 100%)
Does this exist? |
No.
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q
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long arm
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telomere
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present at normal chromatid ends
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constitutive heterochromatin
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condensed in interphase of all cells
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Active doubt
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test Darwin's explanations, correct errors
Who came up with this? |
Thomas Huxley
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Hypothetico Deductivism (falsification)
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1. Gather data (observations about something that is unknown, unexplained, or new)
2. Hypothesize an explanation for those observations. 3. Deduce a consequence of that explanation (a prediction). 4. Formulate an experiment to see if the predicted consequence is observed. Falsification: Theory can be contradicted by an observation or the outcome of a physical experiment. Means falsification can disprove a theory. Doesn't mean theory is wrong though |
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Construct theory
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rational explanation based on measurable natural phenomena
Positive Proof: Yes/No |
No positive proof.
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Parsimony
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simplest explanation is the best working hypothesis
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Complementary Principle
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there are both subjective and objective components to measurement
- Subjective Component (volition): - Objective Component (Cognition): |
Subjective: Questions asked, concepts chosen, measurements chosen
Eg. Electron as a particle and a wave (dual ideas of a single entity) Objective: measurements taken represent the dynamics of the system being studied |
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5 Principles of Ernst Mayr
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1. Evolution as such: The biological world is neither constant nor perpetually cycling, but is steadily and perhaps directionally changing.
2. Common Descent: "all plants and animals have descended from some one form into which life was first breathed" 3. |
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Populational belief
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Population is the lowest level of biological complexity that evolves.
Population is the basic unit of evolutionary change. |
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Lineages
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Ancestor-descendant populations of a series through time
4 Events:? |
1. Persist without change
2. Persist with change 3. Branch 4. Go extinct |
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Divergence of character
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separate lineages accumulate differences from their common ancestor and from each other
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Phylogeny
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the structure of evolutionary history is a branching tree of lineages
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Biogenetic law
Who made this up? |
"ontogeny recapitulates phylogeny"
Ernst Haeckel |
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Terminal addition
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New features are added at the end of ontogeny
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Ontogeny Condensation
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Older features are displaced to earlier and shorter developmental occurrence
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Ontogeny
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development of an organism from zygote to adult
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Which phylum are Humans in?
What trait is this phylum known for? |
Chordata
Notachord trait. What is this trait in humans today? |
Remnants of notachord in humans are the disk bones in our vertebrate
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Tunicates in which phylum?
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Chordata
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All animals share an early developmental stage. What is the order?
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Zygote --> Blastula --> Gastrula
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Heterochrony
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evolutionary change in developmental rates and timing
Eg. Salamanders- aqua form in larvae stage, then terrestrial form in adult stage |
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Heterotropy
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evolutionary change of physical location of a developmental process/module.
Eg. Geckos have toe pads on fingers and toes. (Modified scales) Toe pads initially evolved on toes and fingers but expressed in a different location (tails) |
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Modularity
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characteristic, semi-autonomous patterns of gene expression and celluar proliferation and differentiation
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Module
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An evolving trait that eventually gives rise to other structures
Eg. Vertebrate tail |
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Who coined the word ecology?
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Ernst Haeckel
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Homology (who made this up?)
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The same organ in different organisms under every variety of form and function
Richard Owens (1804-1892) |
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Evolutionary Homology
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forms derived from an equivalent characteristic of a common evolutionary ancestor (molecular and cellular characteristics like homologous DNA)
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ontogeny recapitulates phylogeny
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Haeckel's principle for inferring phylogenies based on the conjectures that evolutionary change adds new features to the end of organismal ontogeny and condenses older features into earlier developmental stages
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Caenogenesis
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Haeckel's term for evolutionary aquisition of new characters at pre-adult stage directly rather than by condensation from an ancestral adult condition
Evolution of new characters that are added to pre-adult states (don't see some characters until adult stage) Eg. Tadpoles --> Frogs, Caterpillar --> Butterfly |
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parsimony
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Methodological principle that the simplest explanation of existing data is the favored working hypothesis; also specifically the phylogenetic principle that the tree structure requiring the smallest amount of character evolution is the best working hypothesis
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Complementarity Principle
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scientific principle derived from the quantum mechanics of Niels Bohr that a scientist must describe both the volitional (subjective) and cognitional ( objective) aspects of measurement
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alignment
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arrangement of homologous DNA sequences to identify specific site or positional homologies
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evolution as such
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Mayr's term for the most basic of Darwin's theories, that the biological world is neither constant nor perpetually cycling, but always changing
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hypothetico-deductivism or falsification
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Formal term for Huxley's prescription that Darwin's theories should be subject to "active doubt" by gathering data that could potentially reject Darwin's conjectures
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common descent
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Mayr's name for Darwin's theory that all our plants and animals have descended from one some form into which life was first breathed
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convergent evolution
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when phenotypes appear similar enough to have two species relation on a tree, but truly they are very genetically different (in older days only phenotypes were used to construct trees and this caused problems)
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Excluding a three-way split, the number of alternative, phylogenetic hypothesis possible for any analysis of three ingroup species and 1 outgroup species is what?
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three
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Distance Methods
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based on statistical principles that group things based on their overall similarity to each other.
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Parsimony Approaches (to form trees)
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group organisms in ways that minimize the number of substitutions that must have occurred since they last shared a common ancestor and are generally invoked only in molecular evolution studies
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Maximum Likelihood(or Bayesian)
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intrinsically probabilistic/statistical and have only become feasible for typical data sets as the raw power of computers increased
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Molecular Homology
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Homologous DNA (diagnosed by high sequence similarity and one copy per haploid genome)
Eg. Forelimb bone structure of chordates |
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Historical structure of sharing homologies
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nested hierarchy of groups within groups
Eg. All those that share vertebrate and there are groups within these |
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sequence of homologous DNA
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many comparisons between humans and chimps
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15 million years ago
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Before molecular homology- the # years ago that the most recent (believed) common ancestor for chimps and humans
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5 million years ago
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Now, thanks to molecular homology- the believed # years ago the most recent common ancestor for chimps & humans
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Monophyletic group (clade)
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a group of 2 or more species/lineages that includes the most recent common ancestor of all members of the group and ALL of its descendants
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MRCA
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most recent common ancestor
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cladogram
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branches denote nested hierarchy of clades as diagnosed by synapomorphies
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phylogenetic tree
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branches denote historical evolutionary lineages
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Are apes a monophyletic group?
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No, if we don't count humans
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assume the simplest tree/ one with least mutations
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parsimony method
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Alignment
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Hypotheses of site homology- usually easiest to align protein-coding DNA
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ancestral state
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present in ingroup and outgroup
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derived state
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present only in the ingroup
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ambiguous
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no sharing of character states between ingroup and outgroup
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parsimony informative characters
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shared derived characteristics
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Parsimony criterion
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Find the tree topology that requires the smallest # of evolutionary changes.
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Genetic difference
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% sequenced difference or % sequenced similarity
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UPGM
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averaging algorithm- quick way to get topology tree
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transversion
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pyrimidine for a purine and vice versa
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transition
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pyrimidine for a pyrimidine and purine for a purine
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transition
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A DNA substitution mutation, purine with purine (A<-->G) and pyrimidine with pyrimidine (C<-->T)
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transversion
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purine with pyrimidine and vise versa
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Ratio of transversion to transition
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Transition 10x more likely than transversion
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Which position of codon is most likely to switch/
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3rd position
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Bayesian operation
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calculate likelihood for contrasting trees
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maximum likelihood method
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evaluate the probability of observing the results in each of the columns considering all possible trees, and measure the likelihood of the entire data set for each contrasting tree.
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2 parallel substitutions on a terminal branch vs. 1 substitution on an internal branch- Which is more likely? Exception?
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2 parallel subs on a terminal branch is more likely (1 change) while 1 sub on internal branch resulted in 2 changes.
However, if the internal branch is shorter compared to the length of the terminal branches, then the 2 ways become equally likely |
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homoplasy
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character similarity that does not represent common ancestry (homoplastic)
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parallelism
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lineages diverge from common ancestor but not from each other
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reversal
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evolutionary return to an ancestral character formerly changed or lost
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convergence
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origin of superficially similar features by dissimilar evolutionary processes- usually pertains to morphology
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Wings are an example of ___ evolution?
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Homoplastic evolution. Wings look similar among organisms but do not represent common ancestry
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three major evolutionary domains
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bacteria, eukarya, archaea
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Transitions vs. Transversion- which is more homoplastic?
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Transitions because character similarity (purine for a purine or pyrimidine for a pyrimidine) does not represent common ancestry
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codon position
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silent vs. replacement sites
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genetic code is degenerate means?
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20 AAs coded by 64 codons
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Silent site
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a codon letter may change but it doesn't change the AA it codes for
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Replacement site
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change in codon letter changes the AA it codes for
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Which # codon does silent substitution?
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Usually 3rd codon
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Bayesian analysis
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each internal branch gets posterior probability
Probability > or = to ? to get strong support? |
p > or = 0.95
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Bootstrapping
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sample sites in an alignment with replacement to produce a new data set equal in size to the original one. For each clade/branch, what % of the trees contain the clade/branch?
If > or = 70%, reject original hypothesis that branch doesn't exist (?) |
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Allopatric speciation
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geographic isolation precedes evolution of species differences
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Outgroup
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allows you to place the root somewhere among the ingroup
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What's the outgroup in the Tree of Life?
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Contains no outgroup because it contains all of life
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endosymbiotic theory of eukaryote origins (who came up with this?)
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mitochondria and chloroplasts are evolutionarily more similar to bacterial genomes than nuclear genomes (the genomes they are found in)
Lynn Margulis |
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Biological Species concept (who?)
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(Mayr) a reproductive community of populations (reproductively isolated from others) that occupies a specific niche in nature.
to determine whether two now distinctly different genetically and phenotypically populations should be considered separate species by testing for Reproductive Barriers |
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Niche
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set of resources actually or potentially used by a population
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Angelman syndrome
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same genotype as Prader-Willi syndrome
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variational theory
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Darwinian evolution is a populational process operating on hereditary differences among organisms within a population
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character polarity
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ancestral-descendant relationships among alternative character states
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5:3 segregation
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postmeiotic segregation present
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empirical verification
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data support a hypothesis as the best working explanation
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trivalent
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usually present in the haploid number in autotriploid
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algorithm
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a process characterized by substrate neutrality, underlying mindlessness, and guaranteed results.
Eg. Natural selection |
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founder event
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A SOURCE OF ALLOPATRY OF POPULATIONS CAUSED BY RARE DISPERSAL OF A FEW ORGANISMS ACROSS A PRE-EXISTING, STRONG GEOGRAPHIC BARRIER
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parsimony informative/phylogenetically informative
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the subset of variable characters in a phylogenetic analysis for which sharing of a derived state (synapmorphy) is observed.
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phylogenetic species concept
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a lineage of ancestral-descendant populations diagnosably distinct from other such lineages.
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postzygotic barrier
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a broad category of reproductive barriers in which hybrid offspring are inviable or sterile, or second-generation offspring suffer these problems
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adaptation
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a character that arose by national selection for a currently observed biological role
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The kind of chromosomal evolutionary change needed to derive the human karyotype from one characteristic of other apes.
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fusion or chromosomal fusion
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A source of allopatry of populations in which formation of a geological barrier subdivides a formerly continuous population
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vicariance
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Exaptation
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Shifts in the function of a trait during evolution
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mathematical model
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an equation that simplifies biological details to identify the critical parameters sufficient for predicting an outcome.
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Blocking factor
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binds to the X chromosome and prevents its inactivation
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Gene-to-Centromere distance
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(#2nd Div Segs)/(2 Total)
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